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<div id="Sx1" class="ltx_section">
<h1 class="ltx_title ltx_title_section">Post-processing analysis</h1>

<div id="Sx1.p1" class="ltx_para">
<p class="ltx_p">ThunderSTORM provides a variety of post-processing methods and tools
which can be applied to the results obtained from previously processed
SMLM data. The software includes methods for correcting the data by
removing molecules with, e.g., poor localization accuracy or small
local density, for merging molecules present in subsequent images,
and for position correction of molecules caused by lateral drift of
the sample and/or by axial stage scanning. Users can also define the
order in which the different post-processing steps are applied. Localization
results can be imported/exported to/from ThunderSTORM in a variety
of data formats which allows full compatibility with other SMLM localization
software.</p>
<ul class="ltx_itemize">
<li id="I1.ix1" class="ltx_item" style="list-style-type:none;">
<span class="ltx_tag ltx_tag_itemize"><em class="ltx_emph">Input:</em></span> 
<div id="I1.ix1.p1" class="ltx_para">
<p class="ltx_p">A list of coordinates with sub-pixel positions
of the molecules.</p>
</div>
</li>
<li id="I1.ix2" class="ltx_item" style="list-style-type:none;">
<span class="ltx_tag ltx_tag_itemize"><em class="ltx_emph">Output:</em></span> 
<div id="I1.ix2.p1" class="ltx_para">
<p class="ltx_p">A corrected list of coordinates with sub-pixel
positions of the molecules.</p>
</div>
</li>
</ul>
</div>
<div id="Sx1.SSx1" class="ltx_subsection">
<h2 class="ltx_title ltx_title_subsection">Guidelines for the choice of parameters</h2>

<div id="Sx1.SSx1.p1" class="ltx_para">
<p class="ltx_p">The order of post-processing steps is user-specified. However, we
recommend the following order: Remove duplicates (if MFA was enabled),
filtering (to remove outliers), Z-stage offset (if applicable), drift
correction, and finally merging.
</p>
</div>
</div>
<div id="Sx1.SSx2" class="ltx_subsection">
<h2 class="ltx_title ltx_title_subsection">See also</h2>

<div id="Sx1.SSx2.p1" class="ltx_para">
<ul id="I2" class="ltx_itemize">
<li id="I2.i1" class="ltx_item" style="list-style-type:none;">
<span class="ltx_tag ltx_tag_itemize">•</span> 
<div id="I2.i1.p1" class="ltx_para">
<p class="ltx_p"><a href="ResultsFilter.html" title="" class="ltx_ref">Filtering according to user-defined criteria</a></p>
</div>
</li>
<li id="I2.i2" class="ltx_item" style="list-style-type:none;">
<span class="ltx_tag ltx_tag_itemize">•</span> 
<div id="I2.i2.p1" class="ltx_para">
<p class="ltx_p"><a href="LocalDensityFilter.html" title="" class="ltx_ref">Local density filter</a></p>
</div>
</li>
<li id="I2.i3" class="ltx_item" style="list-style-type:none;">
<span class="ltx_tag ltx_tag_itemize">•</span> 
<div id="I2.i3.p1" class="ltx_para">
<p class="ltx_p"><a href="DuplicatesFilter.html" title="" class="ltx_ref">Removing duplicates</a></p>
</div>
</li>
<li id="I2.i4" class="ltx_item" style="list-style-type:none;">
<span class="ltx_tag ltx_tag_itemize">•</span> 
<div id="I2.i4.p1" class="ltx_para">
<p class="ltx_p"><a href="ResultsGrouping.html" title="" class="ltx_ref">Merging of reappearing molecules</a></p>
</div>
</li>
<li id="I2.i5" class="ltx_item" style="list-style-type:none;">
<span class="ltx_tag ltx_tag_itemize">•</span> 
<div id="I2.i5.p1" class="ltx_para">
<p class="ltx_p"><a href="ResultsDriftCorrection.html" title="" class="ltx_ref">Lateral drift correction</a></p>
</div>
</li>
<li id="I2.i6" class="ltx_item" style="list-style-type:none;">
<span class="ltx_tag ltx_tag_itemize">•</span> 
<div id="I2.i6.p1" class="ltx_para">
<p class="ltx_p"><a href="ResultsStageOffset.html" title="" class="ltx_ref">Z-stage scanning</a></p>
</div>
</li>
<li id="I2.i7" class="ltx_item" style="list-style-type:none;">
<span class="ltx_tag ltx_tag_itemize">•</span> 
<div id="I2.i7.p1" class="ltx_para">
<p class="ltx_p"><a href="ROIselection.html" title="" class="ltx_ref">ROI selection</a></p>
</div>
</li>
<li id="I2.i8" class="ltx_item" style="list-style-type:none;">
<span class="ltx_tag ltx_tag_itemize">•</span> 
<div id="I2.i8.p1" class="ltx_para">
<p class="ltx_p"><a href="../ImportExportPlugIn.html" title="" class="ltx_ref">Import and export of localization data</a></p>
</div>
</li>
<li id="I2.i9" class="ltx_item" style="list-style-type:none;">
<span class="ltx_tag ltx_tag_itemize">•</span> 
<div id="I2.i9.p1" class="ltx_para">
<p class="ltx_p"><a href="../CBCPlugIn.html" title="" class="ltx_ref">Coordinate based co-localization</a></p>
</div>
</li>
<li id="I2.i10" class="ltx_item" style="list-style-type:none;">
<span class="ltx_tag ltx_tag_itemize">•</span> 
<div id="I2.i10.p1" class="ltx_para">
<p class="ltx_p"><a href="../rendering/ui/Rendering.html" title="" class="ltx_ref">Visualization methods</a></p>
</div>
</li>
</ul>
</div>
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